# Production tasks using the ella-cli

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

This page describes common production tasks that can be performed with the ELLA command line interface (ella-cli).

TIP

The --help flag will show information for most ella-cli commands and options.

# Manage broadcast messages

To add a new broadcast message for all users (shown at the top of the page, e.g. for notifications of planned downtime), run:

ella-cli broadcast new <message>

To deactivate a previously added message, run:

ella-cli broadcast list # get active message_id
ella-cli broadcast deactivate <message_id>

Add the --all or --tail flag to the ella-cli broadcast list command to show all or the last 10 broadcasts, respectively (including inactive).

# Reset user password

To reset the password for a single user, run:

ella-cli users reset_password <username>

This will print a new one-time password to screen, and must be changed upon first new login.

See also Users and passwords.

# Delete analysis

To delete an existing analysis (e.g. wrong import), run:

ella-cli delete analysis <analysis_id>

where analysis_id is the last part of the URL shown in ELLA, e.g. [...]/workflows/analyses/12345.

Note that this will not delete any assessments that have been performed within the analysis; instead, analysis_id is set to NULL in the alleleassessment, referenceassessment, allelereport and geneassessment tables. This means that any associated allele assessments will appear as having been done in a variant workflow (i.e. independent of the analysis) after analysis deletion.

# Delete allele interpretation

To delete interpretation rounds for an individual allele since last finalize, run:

ella-cli delete alleleinterpretation <allele_id>

where allele_id is the last part of the URL shown in ELLA when opening the variant in variant interpretation mode, e.g. [...]/workflows/variants/[...]&allele_id=123

To delete all interpretation rounds (not only since last finalize; use with caution), add the --delete-all flag. This will cascade the delete operation to alleleinterpretationsnapshot, interpretationstatehistory and interpretationlog.

Note that neither option deletes allele assessments (the finalized snapshot that includes a classification, see Datamodel).

Last Updated: 8/21/2020, 11:33:27 AM